An example of coral tissue sampling (image from coralrepository.org).Reef-building corals comprise multipartite symbioses between the cnidarian animal hosts and their associated microbial populations of eukaryotic, prokaryotic, and viral microorganisms forming a coral microbiome, together known as a holobiont. The health of the entire coral holobiont of reefs is being negatively impacted by an increasing variety of environmental and anthropogenic stressors that can cause shifts in the community structure patterns of coral microbiomes. Many corals around the world are being increasingly stressed and degraded or even killed by changing conditions that can lead to greater exposure to pathogens and incidence of bleaching and/or coral disease. The biodiversity of coral reef communities, including biodiversity of the coral microbiomes, can be an important factor involved in coral health and resilience. The establishment of ongoing Genomic Observatories to characterize corals and their microbiomes can be a useful diagnostic and assessment tool to judge the relative health conditions of reefs and assess the effectiveness of management strategies intended to protect them. Such coral genomic observatories can be an extremely useful addition to larger Marine Biodiversity Observing Networks (MBONs) that serve to holistically characterize ecosystem health, status, and trends.
AOML is in the process of developing an integrated Coral Genomics Observing Network (CGON) to collect coral reef community holobiont samples (including coral animal tissue, coral microbiome, and near-coral water samples), to extract and purify total community metagenomics DNA (i.e. the collective environmental DNA from all the organisms in a particular environmental sample), and to conduct metagenomics DNA sequence analysis of all the organisms in these environmental samples, including bacteria, algae, fungi, protists, microscopic eukaryotic larvae, and the coral animals themselves, by the use of state-of-the-art Next-Generation-Sequencing. These coral community characterizations are being conducted for sentinel reef sites along the southeastern Florida coast, in the Florida Keys National Marine Sanctuary, and in other selected sites throughout the Caribbean. It is anticipated that this CGON program will eventually be expanded to include a variety of sentinel coral reef sites around the world and cover a range of critically important and endangered coral species to provide a better understanding of how the coral holobiont/microbiome can influence coral community resilience and adaptation to a wide range of anthropogenic and environmental stressors in the face of changing environmental conditions from climate change, sea level rise, land-based sources of pollution and disease, and ocean acidification. Such a holistic approach to better understand the community genetic factors influencing coral reef resiliency may help managers better predict impacts to coral reefs and to help guide choices of coral species, strains, symbionts, and coral holobiont community structure for use in coral reef restoration efforts. These coral community metagenomic characterization efforts will also serve to add to the community biodiversity measurements and characterization efforts of larger ecosystem-focused Marine Biodiversity Observing Networks, such as the MBON that has been established for the Florida Keys National Marine Sanctuary. CGON sentinel reef observations are also integrated into the on-going ICON and CHAMP programs at AOML.